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(-) Description

Title :  DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH THE BLOOD GROUP A TRISACCHARIDE
 
Authors :  T. W. Hamelryck, R. Loris, J. Bouckaert, G. Strecker, A. Imberty, E. Fernandez, L. Wyns, M. E. Etzler
Date :  30 Jul 98  (Deposition) - 09 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Legume Lectins, Dolichos Biflorus Seed Lectin, Sugar Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. W. Hamelryck, R. Loris, J. Bouckaert, M. H. Dao-Thi, G. Strecker, A. Imberty, E. Fernandez, L. Wyns, M. E. Etzler
Carbohydrate Binding, Quaternary Structure And A Novel Hydrophobic Binding Site In Two Legume Lectin Oligomers From Dolichos Biflorus.
J. Mol. Biol. V. 286 1161 1999
PubMed-ID: 10047489  |  Reference-DOI: 10.1006/JMBI.1998.2534
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LECTIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organ: SEED
    Organism Common: HORSE GRAM
    Organism Scientific: VIGNA UNGUICULATA SUBSP. CYLINDRICA
    Organism Taxid: 3840
    Other Details: DOLICHOS BIFLORUS SEED LECTIN
    Strain: SUBSP. CYLINDRICA
    Synonym: DBL

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2CA2Ligand/IonCALCIUM ION
3MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1A2G4Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2CA-1Ligand/IonCALCIUM ION
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:85 , GLY A:102 , GLY A:103 , TYR A:104 , LEU A:127 , ASN A:129 , GLY A:213 , LEU A:214 , SER A:215 , TYR A:218BINDING SITE FOR RESIDUE A2G A 254
2AC2SOFTWAREASP B:85 , GLY B:102 , GLY B:103 , TYR B:104 , LEU B:127 , ASN B:129 , GLY B:213 , LEU B:214 , SER B:215 , TYR B:218BINDING SITE FOR RESIDUE A2G B 254
3AC3SOFTWAREASP A:125 , LEU A:127 , ASN A:129 , ASP A:133BINDING SITE FOR RESIDUE CA A 301
4AC4SOFTWAREGLU A:123 , ASP A:125 , ASP A:133 , HIS A:138 , SER A:148BINDING SITE FOR RESIDUE MN A 302
5AC5SOFTWAREASP B:125 , LEU B:127 , ASN B:129 , ASP B:133BINDING SITE FOR RESIDUE CA B 301
6AC6SOFTWAREGLU B:123 , ASP B:125 , ASP B:133 , HIS B:138 , SER B:148BINDING SITE FOR RESIDUE MN B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LU2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:84 -Asp A:85
2Ala B:84 -Asp B:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LU2)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC1_VIGUC142-148
 		  2A:120-126
B:120-126
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC1_VIGUC222-231
 		  2A:200-209
B:200-209
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC1_VIGUC142-148
 		  4A:120-126
B:120-126
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC1_VIGUC222-231
 		  4A:200-209
B:200-209

(-) Exons   (0, 0)

(no "Exon" information available for 1LU2)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:253
 aligned with LEC1_VIGUC | P05045 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:253
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   
           LEC1_VIGUC    23 ANIQSFSFKNFNSPSFILQGDATVSSGKLQLTKVKENGIPTPSSLGRAFYSSPIQIYDKSTGAVASWATSFTVKISAPSKASFADGIAFALVPVGSEPRRNGGYLGVFDSDVYNNSAQTVAVEFDTFSNSGWDPSMKHIGIDVNSIKSIATVSWDLANGENAEILITYNAATSLLVASLVHPSRRTSYILSERVDITNELPEYVSVGFSATTGLSEGYIETHDVLSWSFASKLPDDSTAEPLDLASYLVRNVL 275
               SCOP domains d1lu2a_ A: Legume lectin                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1lu2A00 A:1-253  [code=2.60.120.200, no name defined]                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeee..eee..eee..............eeeeee...............eeeeeeeee..........eeeeeeeee........hhh..........hhh..eeeeee............eeeeee.......eee.......eeeeeeeee....eeeeeeeehhh.eeeeeeee..hhhh....eeeeeeeee..........eeeeeeeeeee..........hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG-------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lu2 A   1 ANIQSFSFKNFNSPSFILQGDATVSSGKLQLTKVKENGIPTPSSLGRAFYSSPIQIYDKSTGAVASWATSFTVKISAPSKASFADGIAFALVPVGSEPRRNGGYLGVFDSDVYNNSAQTVAVEFDTLSNSGWDPSMKHIGIDVNSIKSIATVSWDLANGENAEILITYNAATSLLVASLVHPSRRTSYILSERVDITNELPEYVSVGFSATTGLSEGYIETHDVLSWSFASKLPDDSTAEPLDLASYLVRNVL 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   


Chain B from PDB  Type:PROTEIN  Length:253
 aligned with LEC1_VIGUC | P05045 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:253
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   
           LEC1_VIGUC    23 ANIQSFSFKNFNSPSFILQGDATVSSGKLQLTKVKENGIPTPSSLGRAFYSSPIQIYDKSTGAVASWATSFTVKISAPSKASFADGIAFALVPVGSEPRRNGGYLGVFDSDVYNNSAQTVAVEFDTFSNSGWDPSMKHIGIDVNSIKSIATVSWDLANGENAEILITYNAATSLLVASLVHPSRRTSYILSERVDITNELPEYVSVGFSATTGLSEGYIETHDVLSWSFASKLPDDSTAEPLDLASYLVRNVL 275
               SCOP domains d1lu2b_ B: Legume lectin                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1lu2B00 B:1-253  [code=2.60.120.200, no name defined]                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeee..eee..eee..............eeeeee...............eeeeeeeee..........eeeeeeeee........hhh..........hhh..eeeeee............eeeeee......eeee.......eeeeeeeee....eeeeeeee....eeeeeeee..hhhh....eeeeeeeee..........eeeeeeeeeee..........hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG-------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lu2 B   1 ANIQSFSFKNFNSPSFILQGDATVSSGKLQLTKVKENGIPTPSSLGRAFYSSPIQIYDKSTGAVASWATSFTVKISAPSKASFADGIAFALVPVGSEPRRNGGYLGVFDSDVYNNSAQTVAVEFDTLSNSGWDPSMKHIGIDVNSIKSIATVSWDLANGENAEILITYNAATSLLVASLVHPSRRTSYILSERVDITNELPEYVSVGFSATTGLSEGYIETHDVLSWSFASKLPDDSTAEPLDLASYLVRNVL 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1LU2)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LEC1_VIGUC | P05045)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.

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 Related Entries

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UniProtKB/Swiss-Prot
        LEC1_VIGUC | P05045: 1bjq 1lu1

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